Protein homeostasis encompasses the creation, maintenance, and degradation of proteins, and it is essential for organisms to function properly. Yet, environmental stressors can disrupt protein homeostasis, which can lead to protein aggregation. Protein aggregation has been linked to serious aging diseases such as Huntington’s, Parkinson’s, and Alzheimer’s disease. In order to gain a better understanding of the pathways important for maintaining and disrupting protein homeostasis, we subject Caenorhabditis elegans to various environmental stressors that disrupt protein homeostasis. We have found that specific concentrations of hypoxia, or low oxygen conditions, induce an increased amount of protein aggregates in C. elegans compared to animals in room air, suggesting defects in protein homeostasis. In addition, the AMP-activated protein kinase (AMPK) seems to be crucial for allowing the formation of aggregates in hypoxia. AMPK mutants that are placed in hypoxia show a decrease in protein aggregation compared to wild-type animals. Furthermore, another environmental stressor, heat shock, also affects protein homeostasis. Heat shocking C. elegans prior to the hypoxic exposure, decreases the amount of aggregates compared to worms that did not experience heat shock. However, unlike hypoxia-induced protein aggregation, heat shock does not seem to require the presence of functional AMPK in order to influence protein aggregation.

Oxygen (O₂) is essential for aerobic organisms to complete development. However, genetic mechanisms exist to promote development and avoid damage under low oxygen conditions. Elucidating how these mechanisms regulate development is important for understanding diseases, such as ischemia and tumor formation, which have a hypoxic component. We are studying the hypoxic response in Caenorhabditis elegans, a genetically tractable organism that uses simple diffusion for gas exchange with the environment. Previous research has suggested that at 5000ppm O₂, loss-of-function mutations in either the transcription factor hif-1, or an AMP-activated protein kinase (AMPK) subunit aak-2, prematurely arrest development. Given that these two mutants have similar phenotypic responses in severe hypoxia, we hypothesized that aak-2 and hif-1 act in the same genetic pathway to coordinate developmental arrest in hypoxia. To test this, we pharmacologically activated AMPK and performed epistasis analysis with genetic mutations. We found that activating AMPK by treatment with Metformin in a hif-1 mutant was not sufficient to sustain reproductive activity in 5000 ppm O₂. We also generated a strain that constitutively expresses HIF-1 in an aak-2 mutant background and found no difference in developmental arrest from aak-2 mutant animals with wild-type HIF-1 activity. We conclude that aak-2 and hif-1 act in distinct genetic pathways to promote development in hypoxia. Our results suggest that C. elegans has multiple, redundant pathways that coordinate development in hypoxic conditions.

Acute myeloid leukemia (AML) is a type of blood cancer. This disease is treated by chemotherapy and bone marrow transplantation, but mortality rates remain high and new therapies are needed. Because gene expression in AML differs from person to person, it is possible that personalized therapies can be designed by understanding how gene expression predicts drug sensitivity. Previous studies tested the sensitivity of 14 human AML cell lines and 30 primary patient samples to 160 chemotherapy drugs, and utilized computational approaches to identify genes that are correlated with the sensitivity to specific drugs. In my project, I am evaluating several of these predictions by silencing gene expression in AML cell lines with a tool called short hairpin RNA (shRNA), which is used to bind and degrade the expression products of genes called messenger RNA (mRNA). I will then test the ability of drugs to inhibit growth in cells that have undergone gene silencing versus control cells that have not undergone gene silencing. If we successfully validate these gene expression-drug sensitivity relationships, they could lead to personalized clinical treatment approaches in AML.

Autophagy is the process in which eukaryotic cells selectively degrade proteins and organelles. Autophagy has been well documented in organisms ranging from yeast to mammalian cells, with demonstrated roles in response to starvation, aging, and stress. However, there has not been an effective method for measuring autophagy in C. elegans, despite C. elegans being a popular model organism for the study of disease and aging. We refined an assay that uses double-fluorescent protein tagged Atg-8/Lgg-1 to measure autophagy in both yeast as well as C. elegans. This assay reports an increase in autophagy in response to starvation in both model organisms. We then applied this to the study of nematodes containing a mutation in Rheb, an important protein in the upstream signaling cascade that regulates autophagy. Autophagy is damped by signaling through the TORC1 pathway. A mutagenesis screen revealed two different worm mutants (ENU9 and ENU10) which are predicted to hyper-activate TORC1 signaling. Using the aforementioned assay we found that ENU9 and 10 mutants have dramatically reduced levels of autophagy. This work has implications for further research in Alzheimer’s, Parkinson’s and related diseases associated with ageing and proteostasis.

 Although we normally place the academic, institutional gallery or museum exhibition space in a separate domain from the virtual space social sites like Facebook, Tumblr, and Pinterest provide, I argue that the motivations that determine our uses of both spaces are the same. Using the writings of theorists such as Foucault and Baudrillard, and the history of Cabinets of Curiosities, I look critically at the creation of online profiles (primarily related to Facebook, but also found in other popular social sites) and traditional exhibitions spaces (for instance, the galleries of the Museum of Modern Art). I examine the logic of categorization and the intended impact this will have on viewers, comparing the nature of collecting and the curatorial impulse to display, showing that ideas surrounding collection function in both spaces. Through this I illustrate that a curatorial impulse is present in each, revolving around some sense of identity, although there are clear differences in ability to create context and exhibition time frames among other things. This will demonstrate that such spaces provide similar outlets for engrained human behaviors that mediate our interaction with and understanding of not only culture, but social interactions and even personal identity. In effect, I show that these spaces are much more closely related than they have previously been given credit for, and that certain social networking sites might even be the next logical stage in the continual development and progression of our understanding of collecting and exhibiting.

The value of property, especially in an urban environment, is extremely high, yet personal vehicles are given tremendous reign over great swathes of this land. In the historic Belltown area, wide automobile corridors cut through the neighborhood. This vehicle dominated landscape poses safety risks to pedestrians and bicyclists alike while catering to large, single occupancy vehicles. In order to create a safer and more equitable streetscape, certain factors must be taken into consideration. These include reducing parking abundance, restructuring parking prices, correctly allocating road space, and implementing human scale design changes. Through the analysis of the finances of parking, and looking at case study cities, an understanding of better parking management and streetscape design will be formed. I anticipate that the reduction of parking spaces and driving lanes, as well as the introduction of market-rate pricing for parking, will result in less congestion and accidents, will not negatively impact local commerce, and will result in a more inviting streetscape for all users. Furthermore, the fundamental issue of parking is not one that affects the Belltown neighborhood exclusively, but is an issue that persists throughout Seattle and other urban spaces. The core findings of this project may be analyzed and applied to other environments.

The acrosome is a sperm-specific organelle which is best known for its release of digestive enzymes to degrade the egg’s outer membrane during fertilization. Interestingly, it is required for successful fertilization in Drosophila despite the absence of gamete membrane fusion. Here, we show that sperm lacking Pskl, a predicted membrane protein, display irregularly small and round acrosomes, are unable to breakdown the sperm’s plasma membrane after entry into the egg, and prevent the completion of fertilization. Although Pskl's role in acrosome biogenesis is unknown, comparative analysis indicates the pskl gene gains certain groups of exons over evolutionary time. We propose that Pskl has a modular structure and are testing which modules are necessary for subcellular localization and protein function. To determine the minimal requirements for targeting Pskl to the secretory pathway and specifically the acrosomal membrane, we constructed fluorescently tagged deletion derivatives. The results of these studies will be informative for understanding the protein’s complex evolutionary origin and its role in Drosophila-specific features of fertilization.

During spermatogenesis in animals, the developing male germ cell undergoes dramatic changes in nuclear morphology. This transformation of round spermatid nuclei into condensed nuclei of mature sperm is accompanied by loss of histones and enrichment of several sperm-specific chromosomal proteins. To date, the function of only a few sperm-specific chromosomal proteins has been studied. We are using the fruit fly, Drosophila melanogaster, to investigate the function of a protein that is encoded by the CG14835 gene. The protein is interesting because it is small, highly enriched in positively charged amino acids and it contains a small region of similarity to other known sperm-specific chromosomal proteins. To test for the possible requirement of CG14835 for spermatogenesis and male fertility, we are generating mutations by imprecisely excising a transposable element that resides within the gene. Currently, we are molecularly analyzing independent excision lines to identify gene deletions. The phenotype of males deleted for the CG14835 should reveal whether the protein plays a role in sperm chromatin remodeling, sperm success during fertilization, or the maintenance of paternal chromosomes in the early embryo. Overall, these studies should contribute to our understanding of the possible roles that sperm-specific chromosomal proteins play in sperm function.

In this paper, I consider Timothy Morton's idea of ecological thinking and Dipesh Chakrabarty's arguments about humans as geological agents. Both scholars argue for a new mindset in the face of the current climate crisis. For example, Morton attributes our present ecological predicament to the misunderstanding that nature is a separate entity — an object ready to be exploited. We can no longer afford to think this way because industrialization of natural resources has led detrimental effects, everything from climate chaos to species extinction. For Morton though there is hope. If we were able to think more broadly then we could perhaps understand that ecological thought is about coexistence. Similar to Morton, Chakrabarty emphasizes the complex interconnectedness of humans and nature. He maintains that humans can no longer differentiate between human history and natural history, especially since human activity and consumption turned us into geological agents. Guided by these theories, I turn to art — which as Morton states has “something to tell us about the environment.” Art, he suggests can “make us question reality.” To further his point, I compare Albert Bierstadt’s Mount Sir Donald, a late nineteenth century painting, to three contemporary works: Subhankar Banerjee’s Caribou Migration (2002) and Spencer Tunick’s Aletsch Glacier #4, Switzerland (2007), and Camille Seaman’s Grand Pinnacle Iceberg, East Greenland (2006). I use the comparison to question the extent to which our thinking about nature has become transformed — from a nineteenth century notion of the picturesque to a twenty-first century ecological awareness of the environment.

David Maisel changes the terms of environmental art. Black Maps, his recent exhibition at the Western Gallery, demonstrates this shift. In his work, he shifts the syntax, changing the signification of nature within art photography. For example, in his large scale photographic series “Terminal Mirage,” the artist depicts aerial shots of the Great Salt Lake in Utah. These images, at first glance, appear aesthetic with vivid purples, blues, and reds swimming across the picture plane. Yet, upon closer look, a viewer is confronted with the apocalyptic sublime. Through iconography, I will concentrate on how Terminal Mirage 2 is a prime example of his capacity to elicit, initially, the feeling of apocalyptic sublime while the knowledge of context and meaning of the work create a dialogue. Instead, Maisel undermines our ability to understand through obstruction to reveal the themes of his work.

Black Maps: The American Landscape and the Apocalyptic Sublime, a recent show at the Western Gallery, brings together a wide variety of David Maisel's large scale aerial photography. Typically, the artist travels to isolated locals and flies over barren industrialized sites to document the grounds below. Rather than devastation however, Maisel produces breathtaking aesthetic images. For example in Lake Project 20, pulsating red veins run through seductive violet pools that punctuate the surface of the image. While a Greenbergian formalist, through and through, Maisel is also anti Greenbergian, clearly he has concerns for the environment. In my essay I will analyze Maisel's photography highlighting his formalist approach to abstraction. Simultaneously, I will consider the narrative content of his work - which runs counter to his professed aesthetic of formalism. My main point is that Maisel opens a dialogue between visual abstraction and environmental issues. In doing so, he fills viewers with delight and excitement suggesting there is some hope in regards to our recent environmental crisis.

We are interested in identifying the spectrum of mutations that arise when performing the same evolution experiment many times. We have previously grown 32 replicates of haploid yeast cells in continuous cultures under constant sulfur limiting environments for 300 generations. Mutants with increased fitness will increase in prevalence and can be characterized using an array of comparative genomic hybridization (aCGH) or next generation sequencing (NGS). To date we have used aCGH on a subset of our evolutions, and in 16/16 cultures, found amplification of SUL1, a high affinity sulfate ion transporter gene used by the cells to aid in increasing import of sulfate. We are also interested in identifying alternative means for adaptation in this environment and have evolved a a strain in which we'd knocked out SUL1 (sul1Δ). With this background, we observed SUL2 amplification in 4/4 cases in the absence of SUL1. A second focus of our work is to track changes in fitness as specific mutations arise. To assay fitness, we periodically compete an evolving culture against a Green Fluorescent Protein (GFP) expressing ancestral strain of yeast. This work has shown that the dynamics of adaptation of wt and sul1Δ yeast differ, which suggests very different fitness landscapes during the evolution for these two genotypes. Collectively these data show that SUL1 amplification is a first target of evolutionary selection and that in its absence, amplification of SUL2 becomes the primary means for adaptation in constant sulfate limitation.

 Eptesicus fuscus, an insectivorous bat, vocalizes extensively in social communities and during nightly foraging. In their natural environment, bats are frequently exposed to calls from other members of their species. These calls are processed in the bats’ central auditory system, which is highly specialized and adept at processing sounds within the frequency range of its own species’ vocalizations. To investigate the effects of altering the characteristics of the calls that bats were exposed to during postnatal development, we reversibly deafened infant bats with earplugs, presented calls that were higher or lower in frequency range than normal calls, and looked at calls emitted by the bats and physiological changes in the inferior colliculus (IC), the auditory midbrain center. We hypothesized that bats exposed to calls that differed in frequency range from normal calls would learn to vocalize in a frequency range consistent with that to which they were exposed and that there might be a corresponding alteration of the frequency map in the IC. Experimental pups’ earplugs were removed only during the presentation of pre-recorded bat calls that were manipulated in frequency. Following call presentation sessions, vocalizations were recorded. After eight weeks, electrophysiology was used to study the activity of neurons in the IC. The IC is organized tonotopically, meaning that neurons that respond to a particular frequency are grouped together, forming a systematically organized frequency map. While recording neuronal activity, auditory stimuli were presented to determine the preferred frequency of neurons. Using data from recording sites throughout the IC, we found that the tonotopic organization of the experimental pups differed from that of control pups. This implies that after birth, the auditory centers of the brain remain plastic for a period of time and that communication in Eptesicus fuscus is not a purely innate behavior.

Phylogeography is the study of the geographic and spatiotemporal distributions of populations, and it is an important tool for investigating the evolutionary history of species. Determining when and where species originated, merged, or moved is critical in understanding the factors that generate biodiversity. Novel Bayesian phylogeographic methods provide a useful tool for obtaining accurate estimates of these important population dynamic parameters. West Africa is a global biodiversity hotspot with a high number of endemic species, and Agama lizards are a diverse and prominent member of this distinctive ecoregion. To investigate the phylogeography of Agama lizards, I constructed phylogenetic trees from over 300 unique samples of Agama lizards from 20 countries using Bayesian phylogeographic inference. Molecular genetic data from a quickly evolving gene (16S rRNA) provided sufficient variation for estimating the divergences between distinct populations. Visualization of the phylogeographic history for the populations was conducted with Google Earth. This group of species is predicted to have originated in the central part of West Africa (i.e., Cameroon, Nigeria, and Equatorial Guinea). At least five distinctive species formed across the region from that one ancestral population, and one paraphyletic group requires further investigation. Outlining the history of species formation in subtropical West Africa, with an emphasis on when and where populations divided, moved, and reconnected, serves to show the benefits of phylogeographic studies as they can reveal patterns that are otherwise too difficult to detect using other approaches. These studies also serve as tools in providing information for the detection of distinct species.